Fluorescence microscopy (FM) is one of the most important analytical tools in modern life sciences, sufficiently sensitive to allow observation of single molecules. Here we describe the first application of the FM technique for the detection of inorganic environmental pollutants-airborne asbestos fibers that can cause asbestosis, mesothelioma, and lung cancer. In order to assess FM capabilities for detecting and counting asbestos fibers, we screened E. coli lysate for proteins that bind to amphibole asbestos. In combination with the previously discovered E. coli protein DksA (Kuroda et al., Biotechnol. Bioeng. 2008, 99, 285-289) that can specifically bind to chrysotile, the newly identified GatZ protein was used for selective and highly sensitive detection of two different asbestos types. Our novel FM-based method overcomes a number of limitations of the commonly used phase-contrast microscopy (PCM) method, offering a convenient alternative to PCM for airborne asbestos monitoring.